HEADER HYDROLASE 06-NOV-23 8X1B TITLE CRYO-EM STRUCTURE OF FPGALACTOSAMINIDASE FROM FLAVONIFRACTOR PLAUTII TITLE 2 IN APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FPGALACTOSAMINIDASE; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FLAVONIFRACTOR PLAUTII; SOURCE 3 ORGANISM_TAXID: 292800; SOURCE 4 GENE: ERS852411_00574; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS FLAVONIFRACTOR PLAUTII, A TO O TYPE BLOOD, D-(+)-GALACTOSAMINE KEYWDS 2 HYDROCHLORIDE, HYDROLASE EXPDTA ELECTRON MICROSCOPY AUTHOR G.WU,P.HAN,C.SU,M.ZHOU,K.LUO REVDAT 5 02-JUL-25 8X1B 1 JRNL REMARK REVDAT 4 04-JUN-25 8X1B 1 AUTHOR JRNL REVDAT 3 28-MAY-25 8X1B 1 AUTHOR JRNL REVDAT 2 27-NOV-24 8X1B 1 REMARK REVDAT 1 13-NOV-24 8X1B 0 JRNL AUTH M.ZHOU,K.LUO,C.SU,Y.SUN,Z.HUANG,S.MA,X.GAO,J.WANG,C.ZHANG, JRNL AUTH 2 P.HAN,G.WU JRNL TITL STRUCTURAL BASIS OF FPGALNASE AND ITS COMBINATION WITH JRNL TITL 2 FPGALNACDEAC FOR EFFICIENT A-TO-O BLOOD GROUP CONVERSION. JRNL REF EXP HEMATOL ONCOL V. 14 7 2025 JRNL REFN ESSN 2162-3619 JRNL PMID 39856738 JRNL DOI 10.1186/S40164-025-00599-7 REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.590 REMARK 3 NUMBER OF PARTICLES : 673717 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8X1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300041964. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : FPGALACTOSAMINIDASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 49 115.57 -163.30 REMARK 500 ILE A 97 -62.37 -106.97 REMARK 500 ASP A 559 -175.92 62.10 REMARK 500 HIS A 560 26.01 -140.91 REMARK 500 ASN A 656 31.10 -97.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-37989 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF FPGALACTOSAMINIDASE FROM FLAVONIFRACTOR REMARK 900 PLAUTII IN APO STATE DBREF1 8X1B A 44 701 UNP A0A174W4Y6_FLAPL DBREF2 8X1B A A0A174W4Y6 44 701 SEQADV 8X1B LEU A 566 UNP A0A174W4Y PRO 566 ENGINEERED MUTATION SEQRES 1 A 658 TYR ALA ILE ALA GLY ASN GLY VAL ARG VAL THR TYR ASP SEQRES 2 A 658 ALA ASP GLY GLN THR ILE THR LEU TYR ARG THR GLU GLY SEQRES 3 A 658 SER GLY LEU ILE GLN MET SER LYS PRO SER PRO LEU GLY SEQRES 4 A 658 GLY PRO VAL VAL GLY GLY GLN GLU VAL GLN ASP PHE SER SEQRES 5 A 658 HIS ILE SER CYS ASP VAL GLU GLN SER THR SER GLY VAL SEQRES 6 A 658 MET GLY SER GLY GLN ARG MET THR ILE THR SER GLN SER SEQRES 7 A 658 MET SER THR GLY LEU ILE ARG THR TYR VAL LEU GLU THR SEQRES 8 A 658 SER ASP ILE GLU GLU GLY VAL VAL TYR THR ALA THR SER SEQRES 9 A 658 TYR GLU ALA GLY ALA SER ASP VAL GLU VAL SER TRP PHE SEQRES 10 A 658 ILE GLY SER VAL TYR GLU LEU TYR GLY ALA GLU ASP ARG SEQRES 11 A 658 ILE TRP SER TYR ASN GLY GLY GLY GLU GLY PRO MET HIS SEQRES 12 A 658 TYR TYR ASP THR LEU GLN LYS ILE ASP LEU THR ASP SER SEQRES 13 A 658 GLY LYS PHE SER ARG GLU ASN LYS GLN ASP ASP THR ALA SEQRES 14 A 658 ALA SER ILE PRO VAL SER ASP ILE TYR ILE ALA ASP GLY SEQRES 15 A 658 GLY ILE THR VAL GLY ASP ALA SER ALA THR ARG ARG GLU SEQRES 16 A 658 VAL HIS THR PRO VAL GLN GLU THR SER ASP SER ALA GLN SEQRES 17 A 658 VAL SER ILE GLY TRP PRO GLY LYS VAL ILE ALA ALA GLY SEQRES 18 A 658 SER VAL ILE GLU ILE GLY GLU SER PHE ALA VAL VAL HIS SEQRES 19 A 658 PRO GLY ASP TYR TYR ASN GLY LEU ARG GLY TYR LYS ASN SEQRES 20 A 658 ALA MET ASP HIS LEU GLY VAL ILE MET PRO ALA PRO GLY SEQRES 21 A 658 ASP ILE PRO ASP SER SER TYR ASP LEU ARG TRP GLU SER SEQRES 22 A 658 TRP GLY TRP GLY PHE ASN TRP THR ILE ASP LEU ILE ILE SEQRES 23 A 658 GLY LYS LEU ASP GLU LEU GLN ALA ALA GLY VAL LYS GLN SEQRES 24 A 658 ILE THR LEU ASP ASP GLY TRP TYR THR ASN ALA GLY ASP SEQRES 25 A 658 TRP ALA LEU ASN PRO GLU LYS PHE PRO ASN GLY ALA SER SEQRES 26 A 658 ASP ALA LEU ARG LEU THR ASP ALA ILE HIS GLU HIS GLY SEQRES 27 A 658 MET THR ALA LEU LEU TRP TRP ARG PRO CYS ASP GLY GLY SEQRES 28 A 658 ILE ASP SER ILE LEU TYR GLN GLN HIS PRO GLU TYR PHE SEQRES 29 A 658 VAL MET ASP ALA ASP GLY ARG PRO ALA ARG LEU PRO THR SEQRES 30 A 658 PRO GLY GLY GLY THR ASN PRO SER LEU GLY TYR ALA LEU SEQRES 31 A 658 CYS PRO MET ALA ASP GLY ALA ILE ALA SER GLN VAL ASP SEQRES 32 A 658 PHE VAL ASN ARG ALA MET ASN ASP TRP GLY PHE ASP GLY SEQRES 33 A 658 PHE LYS GLY ASP TYR VAL TRP SER MET PRO GLU CYS TYR SEQRES 34 A 658 ASN PRO ALA HIS ASN HIS ALA SER PRO GLU GLU SER THR SEQRES 35 A 658 GLU LYS GLN SER GLU ILE TYR ARG VAL SER TYR GLU ALA SEQRES 36 A 658 MET VAL ALA ASN ASP PRO ASN VAL PHE ASN LEU LEU CYS SEQRES 37 A 658 ASN CYS GLY THR PRO GLN ASP TYR TYR SER LEU PRO TYR SEQRES 38 A 658 MET THR GLN ILE ALA THR ALA ASP PRO THR SER VAL ASP SEQRES 39 A 658 GLN THR ARG ARG ARG VAL LYS ALA TYR LYS ALA LEU MET SEQRES 40 A 658 GLY ASP TYR PHE PRO VAL THR ALA ASP HIS ASN ASN ILE SEQRES 41 A 658 TRP TYR LEU SER ALA VAL GLY THR GLY SER VAL LEU ILE SEQRES 42 A 658 GLU LYS ARG ASP LEU SER GLY THR ALA LYS GLU GLU TYR SEQRES 43 A 658 GLU LYS TRP LEU GLY ILE ALA ASP THR VAL GLN LEU GLN SEQRES 44 A 658 LYS GLY ARG PHE ILE GLY ASP LEU TYR SER TYR GLY PHE SEQRES 45 A 658 ASP PRO TYR GLU THR TYR VAL VAL GLU LYS ASP GLY VAL SEQRES 46 A 658 MET TYR TYR ALA PHE TYR LYS ASP GLY SER LYS TYR SER SEQRES 47 A 658 PRO THR GLY TYR PRO ASP ILE GLU LEU LYS GLY LEU ASP SEQRES 48 A 658 PRO ASN LYS MET TYR ARG ILE VAL ASP TYR VAL ASN ASP SEQRES 49 A 658 ARG VAL VAL ALA THR ASN LEU MET GLY ASP ASN ALA VAL SEQRES 50 A 658 PHE ASN THR ARG PHE SER ASP TYR LEU LEU VAL LYS ALA SEQRES 51 A 658 VAL GLU ILE SER GLU PRO ASP PRO HELIX 1 AA1 ASP A 280 ASP A 293 1 14 HELIX 2 AA2 HIS A 294 GLY A 296 5 3 HELIX 3 AA3 ALA A 301 ILE A 305 5 5 HELIX 4 AA4 THR A 324 LYS A 331 1 8 HELIX 5 AA5 LYS A 331 GLY A 339 1 9 HELIX 6 AA6 GLY A 366 HIS A 380 1 15 HELIX 7 AA7 SER A 397 HIS A 403 1 7 HELIX 8 AA8 PRO A 404 PHE A 407 5 4 HELIX 9 AA9 ALA A 437 ASP A 454 1 18 HELIX 10 AB1 SER A 480 THR A 485 5 6 HELIX 11 AB2 LYS A 487 ASP A 503 1 17 HELIX 12 AB3 ASP A 518 MET A 525 5 8 HELIX 13 AB4 SER A 535 GLY A 551 1 17 HELIX 14 AB5 TRP A 564 THR A 571 1 8 HELIX 15 AB6 GLY A 583 GLN A 600 1 18 SHEET 1 AA1 4 ALA A 45 ILE A 46 0 SHEET 2 AA1 4 VAL A 51 ASP A 56 -1 O VAL A 53 N ILE A 46 SHEET 3 AA1 4 THR A 61 GLU A 68 -1 O THR A 63 N THR A 54 SHEET 4 AA1 4 GLY A 71 GLN A 74 -1 O ILE A 73 N ARG A 66 SHEET 1 AA2 4 ALA A 45 ILE A 46 0 SHEET 2 AA2 4 VAL A 51 ASP A 56 -1 O VAL A 53 N ILE A 46 SHEET 3 AA2 4 THR A 61 GLU A 68 -1 O THR A 63 N THR A 54 SHEET 4 AA2 4 SER A 79 PRO A 80 -1 O SER A 79 N ILE A 62 SHEET 1 AA3 4 SER A 76 LYS A 77 0 SHEET 2 AA3 4 TRP A 159 LEU A 167 -1 O GLU A 166 N LYS A 77 SHEET 3 AA3 4 PRO A 84 VAL A 86 -1 N VAL A 85 O TRP A 159 SHEET 4 AA3 4 GLN A 89 GLU A 90 -1 O GLN A 89 N VAL A 86 SHEET 1 AA4 5 SER A 76 LYS A 77 0 SHEET 2 AA4 5 TRP A 159 LEU A 167 -1 O GLU A 166 N LYS A 77 SHEET 3 AA4 5 ALA A 250 PRO A 257 -1 O TRP A 256 N PHE A 160 SHEET 4 AA4 5 VAL A 239 GLU A 245 -1 N GLN A 244 O GLN A 251 SHEET 5 AA4 5 SER A 203 GLN A 208 -1 N ARG A 204 O VAL A 243 SHEET 1 AA5 9 PHE A 94 GLY A 107 0 SHEET 2 AA5 9 GLY A 110 SER A 121 -1 O ARG A 114 N GLU A 102 SHEET 3 AA5 9 LEU A 126 SER A 135 -1 O ARG A 128 N SER A 119 SHEET 4 AA5 9 VAL A 141 ALA A 150 -1 O TYR A 143 N GLU A 133 SHEET 5 AA5 9 SER A 265 HIS A 277 -1 O ALA A 274 N VAL A 142 SHEET 6 AA5 9 GLY A 226 ASP A 231 -1 N GLY A 230 O PHE A 273 SHEET 7 AA5 9 VAL A 217 TYR A 221 -1 N ILE A 220 O ILE A 227 SHEET 8 AA5 9 ARG A 173 TYR A 177 -1 N TYR A 177 O ASP A 219 SHEET 9 AA5 9 LEU A 191 ASP A 195 -1 O ILE A 194 N ILE A 174 SHEET 1 AA6 2 ARG A 313 TRP A 314 0 SHEET 2 AA6 2 ILE A 576 GLU A 577 1 O GLU A 577 N ARG A 313 SHEET 1 AA7 4 GLN A 342 LEU A 345 0 SHEET 2 AA7 4 THR A 383 TRP A 388 1 O THR A 383 N ILE A 343 SHEET 3 AA7 4 GLY A 459 ASP A 463 1 O LYS A 461 N LEU A 386 SHEET 4 AA7 4 PHE A 507 CYS A 511 1 O LEU A 509 N GLY A 462 SHEET 1 AA8 6 ARG A 605 ILE A 607 0 SHEET 2 AA8 6 GLU A 619 LYS A 625 -1 O GLU A 624 N ARG A 605 SHEET 3 AA8 6 VAL A 628 TYR A 634 -1 O TYR A 630 N VAL A 623 SHEET 4 AA8 6 TYR A 688 ILE A 696 -1 O VAL A 691 N TYR A 631 SHEET 5 AA8 6 MET A 658 ASP A 663 -1 N ARG A 660 O VAL A 694 SHEET 6 AA8 6 ARG A 668 MET A 675 -1 O ARG A 668 N ASP A 663 SHEET 1 AA9 2 ILE A 648 GLU A 649 0 SHEET 2 AA9 2 VAL A 680 PHE A 681 -1 O PHE A 681 N ILE A 648 SSBOND 1 CYS A 511 CYS A 513 1555 1555 2.04 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 CONECT 3581 3595 CONECT 3595 3581 MASTER 120 0 0 15 40 0 0 6 5106 1 2 51 END